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Aim: The aim of the study was to assess the effect of changes in population size and migration on variation in functional immunity genes in the previously bottlenecked population of the grey wolf, Canis lupus. Location: Eastern/Central Europe: Poland, Czechia, Slovakia. Methods: We genotyped 7 immunity genes: three MHC‐DLA genes (dog leukocyte antigen) and four Toll‐like receptor (TLR) genes among 130 wolves originating from three populations: two lowland (Baltic and Central European), and highland Carpathian. We contrasted the population structure in immunity genes with a neutral structure based on 13 microsatellites, and we analysed signatures of selection in the immunity loci. Results: We found high overall genetic variance in immunity genes and no evidence for decreased diversity in the recently established populations. The population structure in immunity loci was weak, with pairwise FST lower than for neutral markers. Although the results of neutrality tests were not significant, we identified codons under selection, both positive and negative. Main Conclusions: We demonstrated that despite recent population expansion which is expected to result in decreased genetic diversity, the diversity of immunity genes in the newly established wolf population is similar to those in the source population. This suggests that migrations do not cause allele loss in grey wolf. Signatures of selection on codon level, but not in tests using allele frequencies, suggest the contrasting effects of demography and selection. [ABSTRACT FROM AUTHOR]